Maybe you can apply the transform using mri_convert or mri_vol2vol created
during autorecon1. Is that what you are looking for?
http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
On Feb 22, 2012, at 11:26 AM, Long wrote:
> Dear all,
>
> I had EPI images and T1 image and the EPI images
Vincent,
Some may look like holes but as you mention are just sulci being cut through by
that plane.
A way to check if it is the above is to put the cursor on the surface that
creates this hole and then toggle to the other views (sagittal, axial,
coronal). It will become clearer whether it is
I don't think there is any other way. Is the talairach really that bad in all
of your data? It won't recon without fixing it?
On Feb 22, 2012, at 6:17 PM, cloud.c...@me.com wrote:
> After reading the tutorial at
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach, I understand
> th
Thanks to Mike's determination, I have found a bug in the way that the
Supratentoral volume in aseg.stats is computed.
A fixed linux version can be obtained from
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.linux
. Copy this into $FREESURFER_HOME/bin/mri_segstats,
Dear Freesurfur users,
I have a question about the design for a surface based analysis! I want to
compare controls and patients. I have 5 covariates. One is a continous
variable. The others are categorial variables (4 with 2 levels and 1 with 5
levels). I want to ajust my result with all of th
Hi,
I am trying to figure out the contrasts to use for a study. I am comparing
age matched patients and controls (all female). The FSGD file has 4
columns, but I'm not sure how to make an appropriate contrast matrix. Any
guidance would be appreciated. I can't seem to find an applicable example
on
hi all
i have still a problem to load an activation map on a pial surface (colin27).
here are the steps followed to this end :
first i run bbregister :
bbregister --s colin27 --mov /home/mlaouche/bashr/V8.nii.gz --init-fsl --reg
/home/mlaouche/bashr/regester1.dat --bold --surf pial
then i u
Total gray matter includes all voxels between the pial and white surface +
subcortical gray matter which are labeled by the aseg.mgz.
Allison
On Thu, 23 Feb 2012, Yolanda Vives wrote:
Dear Freesurfer experts,
In Freesurfer v5.1, aseg.stats files give the value of total gray matter
volume. Is
?h.aparc.stats gives an average in the different labels. You could also
export the labels, then it should give - on average - the same results.
Best,
Martijn
On Wed, Feb 22, 2012 at 9:51 PM, Antonella Kis wrote:
> Dear Marijn,
>
> Thanks again for your help. I tried to do the conversion but I a
Dear All,
I would like to know what is the best way in catching the uncorrected clusters
results from the sig.mgh for a structural study:
Should I use the:
mri_glmfit-sim \
--glmdir lh.GroupAnalysis_Thickness_15.glmdir \
--cache 2 pos \
--cwpvalthresh .99 \
--overwrite
But in this case I am
Hi Dusan, I don't think it is possible. You would have to convert the
sig file into a p-value file, then load it in freeview or tksurfer.
doug
Dusan Hirjak wrote:
> Dear Freesurfer experts,
>
> I am a beginner in using Freesurfer.
>
> I was wondering how "straight p-values" (and not -log(10)p val
Dear Freesurfer experts,
I am a beginner in using Freesurfer.
I was wondering how "straight p-values" (and not -log(10)p value) of a
correlation analysis/comparison between cortical thickeness and age, CPZ,
duration of illness etc. could be displayed on a color bar using "qdec"?
Thanks in
Dear Freesurfer experts,
In Freesurfer v5.1, aseg.stats files give the value of total gray matter
volume. Is this label in the annotation file? How can I know which voxels
from the brain are considered as gray matter?
Thank you in advance,
Yolanda
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